@jbrowse/core 3.0.3 → 3.0.4

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js

@@ -11,7 +11,7 @@ const material_1 = require("@mui/material");
 function HelpDialog({ handleClose, }) {
     return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
-        }, title: "Feature sequence panel help", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { paragraph: true, children: "The \"Feature sequence\" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "For gene features, this panel does special calculations to e.g. stitch together the coding sequence, the options are:" }), (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "CDS - shows the stitched together CDS sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Protein - the translated coding sequence, with the \"standard\" genetic code" }), (0, jsx_runtime_1.jsx)("li", { children: "cDNA - shows the 'copy DNA' of transcript, formed from exon sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Genomic w/ introns +/- Nbp up+down stream - the sequence underlying the entire gene including including introns, with UTR and CDS highlighted" })] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { paragraph: true, children: "For other feature types, the options are:" }), (0, jsx_runtime_1.jsx)("ul", { children: (0, jsx_runtime_1.jsx)("li", { children: "Genomic +/- Nbp up+down stream - the reference genome sequence underlying the feature, with the up and downstream sequence" }) }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["Note 1: you can use the \"gear icon\" ", (0, jsx_runtime_1.jsx)(Settings_1.default, {}), " to edit the number of bp displayed up/downstream and in the intron region"] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note 2: The 'Copy HTML' function retains the colors from the sequence panel but cannot be pasted into some programs like notepad that only expect plain text." })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+        }, title: "Feature sequence panel help", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "The \"Feature sequence\" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "For gene features, this panel does special calculations to e.g. stitch together the coding sequence, the options are:" }), (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "CDS - shows the stitched together CDS sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Protein - the translated coding sequence, with the \"standard\" genetic code" }), (0, jsx_runtime_1.jsx)("li", { children: "cDNA - shows the 'copy DNA' of transcript, formed from exon sequences" }), (0, jsx_runtime_1.jsx)("li", { children: "Genomic w/ introns +/- Nbp up+down stream - the sequence underlying the entire gene including including introns, with UTR and CDS highlighted" })] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "For other feature types, the options are:" }), (0, jsx_runtime_1.jsx)("ul", { children: (0, jsx_runtime_1.jsx)("li", { children: "Genomic +/- Nbp up+down stream - the reference genome sequence underlying the feature, with the up and downstream sequence" }) }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["Note 1: you can use the \"gear icon\" ", (0, jsx_runtime_1.jsx)(Settings_1.default, {}), " to edit the number of bp displayed up/downstream and in the intron region"] }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Note 2: The 'Copy HTML' function retains the colors from the sequence panel but cannot be pasted into some programs like notepad that only expect plain text." })] }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
                         handleClose();
                     }, autoFocus: true, variant: "contained", children: "Close" }) })] }));
 }

package/data_adapters/dataAdapterCache.d.ts

@@ -9,6 +9,6 @@ interface AdapterCacheEntry {
 }
 export declare function getAdapter(pluginManager: PluginManager, sessionId: string, adapterConfigSnapshot: SnapshotIn<AnyConfigurationSchemaType>): Promise<AdapterCacheEntry>;
 export type getSubAdapterType = (adapterConfigSnap: ConfigSnap) => ReturnType<typeof getAdapter>;
-export declare function freeAdapterResources(specification: Record<string, any>): number;
+export declare function freeAdapterResources(args: Record<string, any>): void;
 export declare function clearAdapterCache(): void;
 export {};

package/data_adapters/dataAdapterCache.js

@@ -29,23 +29,20 @@ async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
     cacheEntry.sessionIds.add(sessionId);
     return cacheEntry;
 }
-function freeAdapterResources(specification) {
-    let deleteCount = 0;
-    const specKeys = Object.keys(specification);
+function freeAdapterResources(args) {
+    const specKeys = Object.keys(args);
     if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
-        const { sessionId } = specification;
+        const { sessionId } = args;
         Object.entries(adapterCache).forEach(([cacheKey, cacheEntry]) => {
             cacheEntry.sessionIds.delete(sessionId);
             if (cacheEntry.sessionIds.size === 0) {
-                deleteCount += 1;
                 delete adapterCache[cacheKey];
             }
         });
     }
     else {
         Object.values(adapterCache).forEach(cacheEntry => {
-            const regions = specification.regions ||
-                (specification.region ? [specification.region] : []);
+            const regions = args.regions || (args.region ? [args.region] : []);
             for (const region of regions) {
                 if (region.refName !== undefined) {
                     cacheEntry.dataAdapter.freeResources(region);
@@ -53,7 +50,6 @@ function freeAdapterResources(specification) {
             }
         });
     }
-    return deleteCount;
 }
 function clearAdapterCache() {
     adapterCache = {};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "3.0.3",
+  "version": "3.0.4",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -69,5 +69,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "f516540428282351d26e46743e69a724651bfb2c"
+  "gitHead": "61e6d26f83acbf58a946c2add3415bc46b878df9"
 }

package/pluggableElementTypes/renderers/BoxRendererType.d.ts

@@ -1,35 +1,14 @@
 import FeatureRendererType from './FeatureRendererType';
-import GranularRectLayout from '../../util/layouts/GranularRectLayout';
-import MultiLayout from '../../util/layouts/MultiLayout';
+import { LayoutSession } from './LayoutSession';
 import PrecomputedLayout from '../../util/layouts/PrecomputedLayout';
 import type { RenderArgs as FeatureRenderArgs, RenderArgsDeserialized as FeatureRenderArgsDeserialized, RenderArgsSerialized as FeatureRenderArgsSerialized, RenderResults as FeatureRenderResults, ResultsDeserialized as FeatureResultsDeserialized, ResultsSerialized as FeatureResultsSerialized } from './FeatureRendererType';
-import type { AnyConfigurationModel } from '../../configuration';
-import type { Feature, Region } from '../../util';
-import type SerializableFilterChain from './util/serializableFilterChain';
+import type { LayoutSessionProps } from './LayoutSession';
 import type RpcManager from '../../rpc/RpcManager';
+import type { Feature, Region } from '../../util';
 import type { BaseLayout, SerializedLayout } from '../../util/layouts/BaseLayout';
-export interface LayoutSessionProps {
-    config: AnyConfigurationModel;
-    bpPerPx: number;
-    filters?: SerializableFilterChain;
-}
+import type GranularRectLayout from '../../util/layouts/GranularRectLayout';
+import type MultiLayout from '../../util/layouts/MultiLayout';
 export type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-export interface CachedLayout {
-    layout: MyMultiLayout;
-    config: AnyConfigurationModel;
-    filters?: SerializableFilterChain;
-}
-export declare class LayoutSession implements LayoutSessionProps {
-    config: AnyConfigurationModel;
-    bpPerPx: number;
-    filters?: SerializableFilterChain;
-    constructor(args: LayoutSessionProps);
-    update(props: LayoutSessionProps): void;
-    makeLayout(): MultiLayout<GranularRectLayout<unknown>, unknown>;
-    cachedLayoutIsValid(cachedLayout: CachedLayout): boolean;
-    cachedLayout: CachedLayout | undefined;
-    get layout(): MyMultiLayout;
-}
 export interface RenderArgs extends FeatureRenderArgs {
     bpPerPx: number;
     layoutId: string;
@@ -53,7 +32,12 @@ export interface ResultsDeserialized extends FeatureResultsDeserialized {
     layout: PrecomputedLayout<string>;
 }
 export default class BoxRendererType extends FeatureRendererType {
-    sessions: Record<string, LayoutSession>;
+    layoutSessions: Record<string, LayoutSession>;
+    createLayoutSession(props: LayoutSessionProps): LayoutSession;
+    getLayoutSession(props: {
+        sessionId: string;
+        layoutId: string;
+    }): LayoutSession | undefined;
     getWorkerSession(props: LayoutSessionProps & {
         sessionId: string;
         layoutId: string;
@@ -65,8 +49,9 @@ export default class BoxRendererType extends FeatureRendererType {
         reversed?: boolean | undefined;
         assemblyName: string;
     };
-    createSession(props: LayoutSessionProps): LayoutSession;
-    freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs): Promise<number>;
+    freeResources(args: Record<string, any>): void;
+    freeResourcesInWorker(args: Record<string, any>): void;
+    freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs): Promise<void>;
     deserializeLayoutInClient(json: SerializedLayout): PrecomputedLayout<unknown>;
     deserializeResultsInClient(result: ResultsSerialized, args: RenderArgs): ResultsDeserialized;
     createLayoutInWorker(args: RenderArgsDeserialized): GranularRectLayout<unknown>;

package/pluggableElementTypes/renderers/BoxRendererType.js

@@ -3,62 +3,28 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LayoutSession = void 0;
-const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 const FeatureRendererType_1 = __importDefault(require("./FeatureRendererType"));
+const LayoutSession_1 = require("./LayoutSession");
 const configuration_1 = require("../../configuration");
 const util_1 = require("../../util");
-const GranularRectLayout_1 = __importDefault(require("../../util/layouts/GranularRectLayout"));
-const MultiLayout_1 = __importDefault(require("../../util/layouts/MultiLayout"));
 const PrecomputedLayout_1 = __importDefault(require("../../util/layouts/PrecomputedLayout"));
-class LayoutSession {
-    constructor(args) {
-        this.config = args.config;
-        this.bpPerPx = args.bpPerPx;
-        this.filters = args.filters;
-        this.update(args);
-    }
-    update(props) {
-        Object.assign(this, props);
-    }
-    makeLayout() {
-        return new MultiLayout_1.default(GranularRectLayout_1.default, {
-            maxHeight: (0, configuration_1.readConfObject)(this.config, 'maxHeight'),
-            displayMode: (0, configuration_1.readConfObject)(this.config, 'displayMode'),
-            pitchX: this.bpPerPx,
-            pitchY: (0, configuration_1.readConfObject)(this.config, 'noSpacing') ? 1 : 3,
-        });
-    }
-    cachedLayoutIsValid(cachedLayout) {
-        return (cachedLayout.layout.subLayoutConstructorArgs.pitchX === this.bpPerPx &&
-            (0, fast_deep_equal_1.default)((0, configuration_1.readConfObject)(this.config), cachedLayout.config) &&
-            (0, fast_deep_equal_1.default)(this.filters, cachedLayout.filters));
-    }
-    get layout() {
-        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
-            this.cachedLayout = {
-                layout: this.makeLayout(),
-                config: (0, configuration_1.readConfObject)(this.config),
-                filters: this.filters,
-            };
-        }
-        return this.cachedLayout.layout;
-    }
-}
-exports.LayoutSession = LayoutSession;
 class BoxRendererType extends FeatureRendererType_1.default {
     constructor() {
         super(...arguments);
-        this.sessions = {};
+        this.layoutSessions = {};
+    }
+    createLayoutSession(props) {
+        return new LayoutSession_1.LayoutSession(props);
+    }
+    getLayoutSession(props) {
+        return this.layoutSessions[(0, util_1.getLayoutId)(props)];
     }
     getWorkerSession(props) {
         const key = (0, util_1.getLayoutId)(props);
-        if (!this.sessions[key]) {
-            this.sessions[key] = this.createSession(props);
+        if (!this.layoutSessions[key]) {
+            this.layoutSessions[key] = this.createLayoutSession(props);
         }
-        const session = this.sessions[key];
-        session.update(props);
-        return session;
+        return this.layoutSessions[key].update(props);
     }
     getExpandedRegion(region, renderArgs) {
         const { bpPerPx, config } = renderArgs;
@@ -70,46 +36,65 @@ class BoxRendererType extends FeatureRendererType_1.default {
             end: Math.ceil(region.end + bpExpansion),
         };
     }
-    createSession(props) {
-        return new LayoutSession(props);
+    freeResources(args) {
+        this.freeResourcesInWorker(args);
+    }
+    freeResourcesInWorker(args) {
+        const { regions } = args;
+        const key = (0, util_1.getLayoutId)(args);
+        const session = this.layoutSessions[key];
+        if (session) {
+            const region = regions[0];
+            session.layout.discardRange(region.refName, region.start, region.end);
+        }
     }
     async freeResourcesInClient(rpcManager, args) {
         const { regions } = args;
         const key = (0, util_1.getLayoutId)(args);
-        const session = this.sessions[key];
+        const session = this.layoutSessions[key];
         if (session) {
             const region = regions[0];
             session.layout.discardRange(region.refName, region.start, region.end);
         }
-        return await super.freeResourcesInClient(rpcManager, args);
+        return super.freeResourcesInClient(rpcManager, args);
     }
     deserializeLayoutInClient(json) {
         return new PrecomputedLayout_1.default(json);
     }
     deserializeResultsInClient(result, args) {
         const layout = this.deserializeLayoutInClient(result.layout);
-        return super.deserializeResultsInClient({ ...result, layout }, args);
+        return super.deserializeResultsInClient({
+            ...result,
+            layout,
+        }, args);
     }
     createLayoutInWorker(args) {
         const { regions } = args;
-        const session = this.getWorkerSession(args);
-        return session.layout.getSublayout(regions[0].refName);
+        const { layout } = this.getWorkerSession(args);
+        return layout.getSublayout(regions[0].refName);
     }
     serializeResultsInWorker(results, args) {
-        const serialized = super.serializeResultsInWorker(results, args);
+        const { features, ...rest } = super.serializeResultsInWorker(results, args);
         const region = args.regions[0];
-        serialized.layout = results.layout.serializeRegion(this.getExpandedRegion(region, args));
-        serialized.features = serialized.features.filter(f => {
-            return Boolean(serialized.layout.rectangles[f.uniqueId]);
-        });
-        serialized.maxHeightReached = serialized.layout.maxHeightReached;
-        return serialized;
+        const layout = results.layout.serializeRegion(this.getExpandedRegion(region, args));
+        return {
+            ...rest,
+            layout,
+            maxHeightReached: layout.maxHeightReached,
+            features: features.filter(f => !!layout.rectangles[f.uniqueId]),
+        };
     }
     async render(props) {
         const layout = props.layout ||
             this.createLayoutInWorker(props);
-        const result = await super.render({ ...props, layout });
-        return { ...result, layout };
+        const result = await super.render({
+            ...props,
+            layout,
+        });
+        return {
+            ...result,
+            layout,
+        };
     }
 }
 exports.default = BoxRendererType;

package/pluggableElementTypes/renderers/LayoutSession.d.ts

@@ -0,0 +1,25 @@
+import GranularRectLayout from '../../util/layouts/GranularRectLayout';
+import MultiLayout from '../../util/layouts/MultiLayout';
+import type { AnyConfigurationModel } from '../../configuration';
+import type { Region } from '../../util';
+import type SerializableFilterChain from './util/serializableFilterChain';
+export interface LayoutSessionProps {
+    regions: Region[];
+    config: AnyConfigurationModel;
+    bpPerPx: number;
+    filters?: SerializableFilterChain;
+}
+export type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+export interface CachedLayout {
+    layout: MyMultiLayout;
+    props: LayoutSessionProps;
+}
+export declare class LayoutSession {
+    props: LayoutSessionProps;
+    cachedLayout: CachedLayout | undefined;
+    constructor(props: LayoutSessionProps);
+    update(props: LayoutSessionProps): this;
+    makeLayout(): MultiLayout<GranularRectLayout<unknown>, unknown>;
+    cachedLayoutIsValid(cachedLayout: CachedLayout): boolean;
+    get layout(): MyMultiLayout;
+}

package/pluggableElementTypes/renderers/LayoutSession.js

@@ -0,0 +1,42 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LayoutSession = void 0;
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const configuration_1 = require("../../configuration");
+const GranularRectLayout_1 = __importDefault(require("../../util/layouts/GranularRectLayout"));
+const MultiLayout_1 = __importDefault(require("../../util/layouts/MultiLayout"));
+class LayoutSession {
+    constructor(props) {
+        this.props = props;
+    }
+    update(props) {
+        this.props = props;
+        return this;
+    }
+    makeLayout() {
+        return new MultiLayout_1.default(GranularRectLayout_1.default, {
+            maxHeight: (0, configuration_1.readConfObject)(this.props.config, 'maxHeight'),
+            displayMode: (0, configuration_1.readConfObject)(this.props.config, 'displayMode'),
+            pitchX: this.props.bpPerPx,
+            pitchY: (0, configuration_1.readConfObject)(this.props.config, 'noSpacing') ? 1 : 3,
+        });
+    }
+    cachedLayoutIsValid(cachedLayout) {
+        return (cachedLayout.props.bpPerPx === this.props.bpPerPx &&
+            (0, fast_deep_equal_1.default)((0, configuration_1.readConfObject)(this.props.config), (0, configuration_1.readConfObject)(cachedLayout.props.config)) &&
+            (0, fast_deep_equal_1.default)(this.props.filters, cachedLayout.props.filters));
+    }
+    get layout() {
+        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+            this.cachedLayout = {
+                layout: this.makeLayout(),
+                props: this.props,
+            };
+        }
+        return this.cachedLayout.layout;
+    }
+}
+exports.LayoutSession = LayoutSession;

package/pluggableElementTypes/renderers/RendererType.d.ts

@@ -21,5 +21,5 @@ export default class RendererType extends PluggableElementBase {
         pluginManager: PluginManager;
     });
     render(props: RenderProps): Promise<RenderResults>;
-    freeResources(): number;
+    freeResources(_args: any): void;
 }

package/pluggableElementTypes/renderers/RendererType.js

@@ -18,8 +18,6 @@ class RendererType extends PluggableElementBase_1.default {
             reactElement: (0, jsx_runtime_1.jsx)(this.ReactComponent, { ...props }),
         };
     }
-    freeResources() {
-        return 0;
-    }
+    freeResources(_args) { }
 }
 exports.default = RendererType;

package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts

@@ -44,6 +44,6 @@ export default class ServerSideRenderer extends RendererType {
     serializeResultsInWorker(results: RenderResults, args: RenderArgsDeserialized): ResultsSerialized;
     renderInClient(rpcManager: RpcManager, args: RenderArgs): Promise<ResultsSerialized>;
     renderInWorker(args: RenderArgsSerialized): Promise<ResultsSerialized>;
-    freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs): Promise<number>;
+    freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs): Promise<void>;
 }
 export { type RenderResults } from './RendererType';

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -75,9 +75,8 @@ class ServerSideRenderer extends RendererType_1.default {
     }
     async freeResourcesInClient(rpcManager, args) {
         const serializedArgs = this.serializeArgsInClient(args);
-        const freed = this.freeResources();
-        const freedRpc = (await rpcManager.call(args.sessionId, 'CoreFreeResources', serializedArgs));
-        return freed + freedRpc;
+        const { sessionId } = args;
+        await rpcManager.call(sessionId, 'CoreFreeResources', serializedArgs);
     }
 }
 exports.default = ServerSideRenderer;

package/rpc/methods/CoreFreeResources.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodType from '../../pluggableElementTypes/RpcMethodType';
 export default class CoreFreeResources extends RpcMethodType {
     name: string;
-    execute(specification: Record<string, unknown>): Promise<number>;
+    execute(args: Record<string, unknown>): Promise<void>;
     serializeArguments(args: Record<string, unknown>, _rpcDriver: string): Promise<Record<string, unknown>>;
 }

package/rpc/methods/CoreFreeResources.js

@@ -10,16 +10,11 @@ class CoreFreeResources extends RpcMethodType_1.default {
         super(...arguments);
         this.name = 'CoreFreeResources';
     }
-    async execute(specification) {
-        let deleteCount = 0;
-        deleteCount += (0, dataAdapterCache_1.freeAdapterResources)(specification);
+    async execute(args) {
+        (0, dataAdapterCache_1.freeAdapterResources)(args);
         this.pluginManager.getRendererTypes().forEach(renderer => {
-            const count = renderer.freeResources();
-            if (count) {
-                deleteCount += count;
-            }
+            renderer.freeResources(args);
         });
-        return deleteCount;
     }
     async serializeArguments(args, _rpcDriver) {
         return args;

package/rpc/methods/CoreGetFeatureDetails.js

@@ -31,7 +31,7 @@ class CoreGetFeatureDetails extends RpcMethodType_1.default {
         const { rendererType, featureId } = deserializedArgs;
         const RendererType = this.pluginManager.getRendererType(rendererType);
         return {
-            feature: (_b = (_a = RendererType.sessions[(0, util_1.getLayoutId)(args)]) === null || _a === void 0 ? void 0 : _a.cachedLayout.layout.getDataByID(featureId)) === null || _b === void 0 ? void 0 : _b.toJSON(),
+            feature: (_b = (_a = RendererType.getLayoutSession(args)) === null || _a === void 0 ? void 0 : _a.cachedLayout.layout.getDataByID(featureId)) === null || _b === void 0 ? void 0 : _b.toJSON(),
         };
     }
 }